How to unlink / remove an object from a scene?
While the active scene is Scene.001 select Cube.001 and press X. You can also right-click   on the object in the outliner and choose Delete.

Deleting an object only applies to the current scene, any other "copies" in other scenes will still remain there.

You can link the object back to Scene.001 by selecting it in Scene and pressing &#9096; CtrlL->Objects to Scene->Scene.001

You can also remove the object using python, you can type the following into blender's python console or paste it into blender's text editor and click run script. Changing unlink to link will let you replace the object back into Scene.001.

bpy.data.scenes['Scene.001'].objects.unlink(bpy.data.objects['Cube.001'])